Calcium in PDB 2vdq: Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv

The structure of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv, PDB code: 2vdq was solved by T.A.Springer, J.Zhu, T.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.63 / 2.59
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.331, 148.331, 176.567, 90.00, 90.00, 120.00
R / Rfree (%)	14.1 / 19

The structure of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv (pdb code 2vdq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv, PDB code: 2vdq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:58.1 occ:1.00 OD2 A:ASP245 2.3 52.4 1.0 OE1 A:GLU252 2.4 48.3 1.0 O A:THR250 2.4 48.9 1.0 OG1 A:THR250 2.4 47.0 1.0 OE1 A:GLU243 2.5 36.4 1.0 O A:ASP247 2.5 54.9 1.0 OE2 A:GLU252 2.5 46.5 1.0 OE2 A:GLU243 2.6 36.3 1.0 CD A:GLU252 2.8 47.4 1.0 CD A:GLU243 2.9 37.8 1.0 C A:THR250 3.1 47.1 1.0 CG A:ASP245 3.1 52.3 1.0 CB A:THR250 3.5 49.2 1.0 OD1 A:ASP245 3.5 53.7 1.0 C A:ASP247 3.5 58.1 1.0 CA A:THR250 3.7 49.5 1.0 N A:THR250 4.0 54.2 1.0 N A:THR251 4.0 45.2 1.0 N A:ASP247 4.1 58.2 1.0 CA A:ASP247 4.2 59.5 1.0 CG A:GLU252 4.3 46.1 1.0 CB A:ASP245 4.3 51.1 1.0 CG A:GLU243 4.3 37.4 1.0 CA A:THR251 4.3 47.5 1.0 N A:ASP245 4.3 49.4 1.0 CB A:ASP247 4.4 60.9 1.0 N A:LEU248 4.5 61.1 1.0 C A:THR251 4.6 46.1 1.0 N A:GLU252 4.6 44.2 1.0 CA A:ASP245 4.7 50.1 1.0 CA A:GLU243 4.7 38.8 1.0 N A:PHE244 4.7 42.3 1.0 N A:GLY246 4.7 53.6 1.0 C A:ASP245 4.8 51.8 1.0 CG2 A:THR250 4.8 50.2 1.0 CA A:LEU248 4.8 63.1 1.0 O A:HOH4286 4.8 64.2 1.0 CB A:GLU243 4.9 37.5 1.0 C A:LEU248 5.0 61.6 1.0

Calcium binding site 2 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:49.3 occ:1.00 O A:HOH4359 2.2 43.6 1.0 OD1 A:ASN299 2.3 50.2 1.0 OD1 A:ASP297 2.3 50.3 1.0 O A:ARG303 2.4 51.2 1.0 OD1 A:ASP301 2.5 43.2 1.0 OD1 A:ASP305 2.6 38.7 1.0 OD2 A:ASP305 2.6 42.5 1.0 CG A:ASP305 2.9 41.6 1.0 CG A:ASN299 3.3 44.9 1.0 CG A:ASP301 3.4 41.9 1.0 CG A:ASP297 3.4 48.8 1.0 C A:ARG303 3.5 52.1 1.0 OD2 A:ASP301 3.6 40.7 1.0 ND2 A:ASN299 3.9 41.8 1.0 N A:ARG303 4.1 50.6 1.0 CB A:ARG303 4.1 55.1 1.0 CA A:ARG303 4.1 52.7 1.0 CB A:ASP297 4.2 48.1 1.0 N A:ASN299 4.2 42.1 1.0 CA A:ASP297 4.2 47.5 1.0 OD2 A:ASP297 4.2 46.0 1.0 N A:VAL298 4.3 45.4 1.0 CB A:ASP305 4.4 42.4 1.0 CB A:ASN299 4.5 42.4 1.0 N A:ASP305 4.6 46.2 1.0 N A:ASP301 4.6 40.6 1.0 C A:ASP297 4.6 47.1 1.0 C A:HIS304 4.6 48.1 1.0 CD2 A:LEU332 4.6 47.2 1.0 N A:HIS304 4.7 51.3 1.0 CB A:ASP301 4.7 43.3 1.0 CA A:ASN299 4.7 41.3 1.0 O A:GLN333 4.8 48.7 1.0 C A:ASN299 4.8 40.2 1.0 N A:GLN333 4.9 49.8 1.0 N A:GLY300 4.9 42.2 1.0 O A:HIS304 4.9 46.3 1.0 CA A:ASP305 4.9 44.3 1.0 CA A:HIS304 5.0 50.2 1.0 N A:GLY302 5.0 48.8 1.0

Calcium binding site 3 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:64.3 occ:1.00 OD1 A:ASP367 2.3 50.6 1.0 O A:HOH4391 2.3 61.6 1.0 O A:TYR371 2.4 49.6 1.0 OD2 A:ASP365 2.5 48.1 1.0 OD1 A:ASP369 2.6 54.1 1.0 OD2 A:ASP373 2.6 54.5 1.0 OD1 A:ASP373 2.6 58.0 1.0 CG A:ASP373 3.0 55.9 1.0 CG A:ASP369 3.4 50.0 1.0 CG A:ASP367 3.4 51.5 1.0 C A:TYR371 3.6 49.4 1.0 CG A:ASP365 3.6 49.5 1.0 OD2 A:ASP369 3.7 49.9 1.0 OD2 A:ASP367 4.0 54.5 1.0 N A:ASP367 4.1 50.2 1.0 N A:LEU366 4.3 50.8 1.0 N A:TYR371 4.3 47.5 1.0 CA A:ASP365 4.3 50.9 1.0 N A:ASP369 4.3 49.6 1.0 CA A:TYR371 4.3 48.9 1.0 OD1 A:ASP365 4.3 48.7 1.0 CB A:TYR371 4.4 46.4 1.0 CD2 A:LEU393 4.5 49.2 1.0 C A:ASP365 4.5 50.7 1.0 CB A:ASP369 4.5 48.7 1.0 CB A:ASP373 4.5 52.8 1.0 N A:ARG368 4.5 53.3 1.0 CB A:ASP365 4.6 50.4 1.0 N A:ASN372 4.6 49.1 1.0 C A:ASN372 4.6 51.8 1.0 CB A:ASP367 4.6 50.8 1.0 CA A:ASP367 4.7 50.8 1.0 CA A:ASN372 4.7 50.5 1.0 C A:ASP367 4.8 51.4 1.0 O A:ASN372 4.8 56.4 1.0 CB A:LEU393 4.8 51.1 1.0 N A:ASP373 4.8 50.9 1.0 N A:GLY394 4.8 51.5 1.0 CA A:ASP369 4.9 48.5 1.0 O A:GLY394 5.0 47.0 1.0

Calcium binding site 4 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:57.1 occ:1.00 OD1 A:ASN430 2.2 49.6 1.0 O A:HOH4436 2.2 47.2 1.0 O A:TYR432 2.3 50.8 1.0 OD1 A:ASP426 2.3 54.3 1.0 OD1 A:ASP428 2.4 54.0 1.0 OD2 A:ASP434 2.5 47.0 1.0 OD1 A:ASP434 2.7 50.0 1.0 CG A:ASP434 2.9 48.0 1.0 CG A:ASN430 3.2 47.2 1.0 CG A:ASP426 3.4 53.9 1.0 C A:TYR432 3.4 51.5 1.0 CG A:ASP428 3.5 53.1 1.0 ND2 A:ASN430 3.9 48.1 1.0 OD2 A:ASP428 3.9 53.9 1.0 N A:TYR432 4.0 51.0 1.0 O A:ALA450 4.1 57.2 1.0 CA A:TYR432 4.1 51.0 1.0 CB A:ASN430 4.2 47.5 1.0 OD2 A:ASP426 4.2 52.9 1.0 N A:ASN430 4.2 49.8 1.0 CB A:TYR432 4.3 51.1 1.0 CA A:ASP426 4.3 55.0 1.0 CB A:ASP426 4.3 53.5 1.0 CB A:ASP434 4.4 48.0 1.0 N A:ASP428 4.4 54.0 1.0 N A:PRO433 4.5 53.6 1.0 N A:ILE427 4.5 54.5 1.0 N A:ALA450 4.6 53.3 1.0 C A:PRO433 4.6 53.9 1.0 CA A:ASN430 4.6 48.5 1.0 N A:ASP429 4.7 53.8 1.0 C A:ASP426 4.7 55.5 1.0 N A:ASP434 4.7 52.3 1.0 N A:GLY431 4.7 50.9 1.0 CA A:PRO433 4.7 53.9 1.0 CB A:ASP428 4.7 51.7 1.0 C A:ASN430 4.9 49.1 1.0 O A:PRO433 4.9 56.1 1.0 CA A:ASP428 4.9 52.5 1.0 CB A:ALA450 5.0 54.7 1.0

Calcium binding site 5 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:35.9 occ:1.00 OD1 B:ASP127 2.2 46.4 1.0 OD2 B:ASP251 2.3 47.8 1.0 O C:HOH4013 2.3 34.5 1.0 OD1 B:ASP126 2.3 56.6 1.0 O B:SER123 2.5 42.6 1.0 O1 B:GOL1462 2.7 57.1 1.0 O2 B:GOL1462 2.8 54.1 1.0 C2 B:GOL1462 3.0 55.7 1.0 CG B:ASP126 3.3 57.7 1.0 CG B:ASP127 3.4 44.7 1.0 CG B:ASP251 3.4 48.9 1.0 C1 B:GOL1462 3.4 55.8 1.0 OD2 B:ASP126 3.5 61.8 1.0 C B:SER123 3.5 43.6 1.0 CB B:ASP251 3.9 47.3 1.0 OD2 B:ASP127 4.0 43.8 1.0 O B:HOH4061 4.2 57.8 1.0 N B:MET124 4.3 44.0 1.0 C3 B:GOL1462 4.4 57.5 1.0 CA B:MET124 4.4 43.3 1.0 CA B:SER123 4.4 43.0 1.0 OD1 B:ASP251 4.4 50.2 1.0 CB B:SER123 4.5 42.3 1.0 CB B:ASP127 4.5 44.9 1.0 O3 B:GOL1462 4.6 58.2 1.0 O B:HOH4307 4.7 59.6 1.0 CB B:ASP126 4.7 52.7 1.0 N B:ASP127 4.8 49.0 1.0 OXT C:VAL411 4.8 51.9 1.0 O B:HOH4308 4.8 62.5 1.0 N B:ASP126 5.0 48.2 1.0

Calcium binding site 6 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:34.9 occ:1.00 OD1 B:ASP217 2.2 39.3 1.0 OD1 B:ASN215 2.2 42.3 1.0 O B:PRO219 2.3 47.5 1.0 OD2 B:ASP158 2.3 43.2 1.0 OE2 B:GLU220 2.3 42.4 1.0 O B:ASP217 2.4 39.8 1.0 CG B:ASP217 3.2 41.3 1.0 CG B:ASN215 3.4 42.8 1.0 C B:ASP217 3.4 40.7 1.0 C B:PRO219 3.4 41.4 1.0 CG B:ASP158 3.4 42.6 1.0 CD B:GLU220 3.4 45.3 1.0 CB B:ASP158 3.8 41.7 1.0 CA B:GLU220 3.8 43.4 1.0 ND2 B:ASN215 3.8 42.6 1.0 OD2 B:ASP217 3.9 42.3 1.0 NE2 B:HIS255 4.0 43.3 1.0 CA B:ASP217 4.0 39.6 1.0 N B:GLU220 4.0 42.2 1.0 N B:ASP217 4.0 40.3 1.0 OE1 B:GLU220 4.2 43.9 1.0 CB B:ASP217 4.2 38.9 1.0 C B:ALA218 4.3 39.2 1.0 CD2 B:HIS255 4.3 44.0 1.0 N B:PRO219 4.3 39.9 1.0 O B:ALA218 4.4 38.4 1.0 N B:ALA218 4.4 41.3 1.0 CG B:GLU220 4.4 43.8 1.0 CA B:PRO219 4.5 40.5 1.0 OD1 B:ASP158 4.5 40.7 1.0 CB B:GLU220 4.5 43.9 1.0 CB B:ASN215 4.6 41.0 1.0 CA B:ALA218 4.8 39.5 1.0 CD B:PRO219 4.8 40.4 1.0 C B:GLU220 4.9 43.8 1.0 CD2 B:TYR164 4.9 45.2 1.0 CB B:TYR164 4.9 45.0 1.0

T.A.Springer, J.Zhu, T.Xiao. Structural Basis For Distinctive Recognition of Fibrinogen Gammac Peptide By the Platelet Integrin ALPHAIIBBETA3. J.Cell Biol. V. 182 791 2008.
ISSN: ISSN 0021-9525
PubMed: 18710925
DOI: 10.1083/JCB.200801146